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- PDB-8wq3: Crystal structure of the C-terminal RRM domain of an RBP -

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Basic information

Entry
Database: PDB / ID: 8wq3
TitleCrystal structure of the C-terminal RRM domain of an RBP
ComponentsRNA-binding protein 45
KeywordsRNA BINDING PROTEIN / RBM45 / RRM / ALS / FTLD
Function / homology
Function and homology information


nervous system development / cell differentiation / ribonucleoprotein complex / RNA binding / nucleoplasm / identical protein binding / nucleus / cytoplasm
Similarity search - Function
RBM45, RNA recognition motif 1 / RBM45, RNA recognition motif 2 / RBM45, RNA recognition motif 3 / RBM45, RNA recognition motif 4 / RNA recognition motif / RNA recognition motif / Eukaryotic RNA Recognition Motif (RRM) profile. / RNA recognition motif domain / RNA-binding domain superfamily / Nucleotide-binding alpha-beta plait domain superfamily
Similarity search - Domain/homology
RNA-binding protein 45
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.41 Å
AuthorsChen, X. / Jiang, M. / Yang, Z. / Chen, X. / Wei, Q. / Guo, S. / Wang, M.
Funding support China, 1items
OrganizationGrant numberCountry
Other government2108085MC75 China
CitationJournal: J.Biol.Chem. / Year: 2024
Title: Structural basis for RNA recognition by the C-terminal RRM domain of human RBM45.
Authors: Chen, X. / Wei, Q. / Yang, Z. / Chen, X. / Guo, S. / Jiang, M. / Wang, M.
History
DepositionOct 10, 2023Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Aug 21, 2024Provider: repository / Type: Initial release
Revision 1.1Sep 18, 2024Group: Database references / Category: citation / Item: _citation.journal_volume

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: RNA-binding protein 45
B: RNA-binding protein 45
C: RNA-binding protein 45
D: RNA-binding protein 45
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,1686
Polymers53,0974
Non-polymers712
Water3,945219
1
A: RNA-binding protein 45


Theoretical massNumber of molelcules
Total (without water)13,2741
Polymers13,2741
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: RNA-binding protein 45


Theoretical massNumber of molelcules
Total (without water)13,2741
Polymers13,2741
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: RNA-binding protein 45


Theoretical massNumber of molelcules
Total (without water)13,2741
Polymers13,2741
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: RNA-binding protein 45
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,3453
Polymers13,2741
Non-polymers712
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)71.261, 74.602, 195.843
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein
RNA-binding protein 45 / Developmentally-regulated RNA-binding protein 1 / RB-1 / RNA-binding motif protein 45


Mass: 13274.352 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: RBM45, DRB1, DRBP1 / Plasmid: pET22b / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q8IUH3
#2: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 219 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.45 Å3/Da / Density % sol: 54.43 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: 18% v/v 2-Propanol, 0.1 M Sodium chloride basic dihydrate pH 5.5, and 20% w/v Polyethylene glycol 4000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.97915 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Aug 22, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97915 Å / Relative weight: 1
ReflectionResolution: 2.4→50 Å / Num. obs: 20694 / % possible obs: 100 % / Redundancy: 9.7 % / CC1/2: 1 / CC star: 1 / Rmerge(I) obs: 0.148 / Rpim(I) all: 0.05 / Rrim(I) all: 0.156 / Χ2: 0.981 / Net I/σ(I): 5.1
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2CC starRpim(I) allRrim(I) allΧ2% possible all
2.4-2.4910.21.35720290.7140.9130.4441.4290.926100
2.49-2.59101.03620540.7910.940.3431.0930.948100
2.59-2.79.60.68820430.8760.9660.2320.7270.988100
2.7-2.859.80.53420400.9350.9830.1780.5631.001100
2.85-3.029.60.35820480.960.990.1210.3780.999100
3.02-3.26100.23920470.9790.9950.0790.2521.026100
3.26-3.589.60.14320400.9920.9980.0480.1510.967100
3.58-4.19.70.0920790.9960.9990.030.0950.999100
4.1-5.179.60.06221210.9970.9990.0210.0660.949100
5.17-508.90.05521930.99910.0190.0581.00699.7

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Processing

Software
NameVersionClassification
PHENIX(1.20.1_4487: ???)refinement
HKL-3000data scaling
HKL-3000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.41→35.49 Å / SU ML: 0.37 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 24.66 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2205 1035 5.08 %
Rwork0.1827 --
obs0.1846 20388 98.69 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.41→35.49 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3069 0 2 219 3290
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.004
X-RAY DIFFRACTIONf_angle_d0.694
X-RAY DIFFRACTIONf_dihedral_angle_d12.4111192
X-RAY DIFFRACTIONf_chiral_restr0.05497
X-RAY DIFFRACTIONf_plane_restr0.006542
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.41-2.530.35361480.28462656X-RAY DIFFRACTION97
2.53-2.690.29211500.24672695X-RAY DIFFRACTION97
2.69-2.90.29221490.23672734X-RAY DIFFRACTION99
2.9-3.190.26761360.22812756X-RAY DIFFRACTION99
3.19-3.650.22811360.18312803X-RAY DIFFRACTION100
3.66-4.60.17971500.14182802X-RAY DIFFRACTION100
4.6-35.490.17631660.15052907X-RAY DIFFRACTION99

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